createPhenotype {patternize}

Plot color pattern prediction for specified PCA values

Description

Plot color pattern prediction for specified PCA values

Usage

createPhenotype(
  PCAdata,
  PCApredict,
  IDlist,
  rasterList,
  colpalette = NULL,
  plotCartoon = FALSE,
  refShape = NULL,
  outline = NULL,
  lines = NULL,
  landList = NULL,
  adjustCoords = FALSE,
  cartoonID = NULL,
  normalized = TRUE,
  crop = c(0, 0, 0, 0),
  flipRaster = NULL,
  flipOutline = NULL,
  imageList = NULL,
  cartoonOrder = "above",
  lineOrder = "above",
  cartoonCol = "gray",
  cartoonFill = NULL,
  legendTitle = "Proportion",
  zlim = NULL
)

Arguments

PCAdata

Output of PCA analysis. List item 3 of patPCA.

PCApredict

A vector with the PCA values for which to predict the phenotype. This vector only needs to include the values upto the last PCA axis to predict along, other values are set to zero.

IDlist

List of sample IDs.

rasterList

rasterList used for PCA.

colpalette

Vector of colors for color palette (default = c("white","lightblue","blue","green", "yellow","red"))

plotCartoon

Whether to plot a cartoon. This cartoon should be drawn on one of the samples used in the analysis.

refShape

This can be 'target' in case the reference shape is a single sample (for registration analysis) or 'mean' if the images were transformed to a mean shape (only for meanshape when using landmark transformation)

outline

xy coordinates that define outline.

lines

list of files with xy coordinates of line objects to be added to cartoon.

landList

Landmark landmarkList.

adjustCoords

Adjust landmark coordinates.

cartoonID

ID of the sample for which the cartoon was drawn.

normalized

Set this to true in case the summed rasters are already devided by the sample number.

crop

Vector c(xmin, xmax, ymin, ymax) that specifies the pixel coordinates to crop the original image used in landmark or registration analysis.

flipRaster

Whether to flip raster along xy axis (in case there is an inconsistency between raster and outline coordinates).

flipOutline

Whether to flip plot along x, y or xy axis.

imageList

List of images should be given if one wants to flip the outline or adjust landmark coordinates.

cartoonOrder

Whether to plot the cartoon outline 'above' or 'under' the pattern raster (default = 'above'). Set to 'under' for filled outlines.

lineOrder

Whether to plot the cartoon lines 'above' or 'under' the pattern raster (default = 'above').

cartoonCol

Outline and line color for cartoon (deafault = 'gray').

cartoonFill

Fill color for outline of cartoon (default = NULL).

legendTitle

Title of the raster legend (default = 'Proportion').

zlim

zlim values for predicted pattern.